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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ), 'gf_id' => 'HOM05D001150', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001150' ), 'data_identifier' => 'HOM05D001150', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001150', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '538', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p22880' => 'bna', 'A01p30470' => 'bna', 'A02p24920' => 'bna', 'A03p49120' => 'bna', 'A04p00110' => 'bna', 'A08p11760' => 'bna', 'A10p01700' => 'bna', 'Aa31LG10G17160' => 'aar', 'Aa31LG1G9460' => 'aar', 'Aa31LG9G1960' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.3620' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2442' => 'aag', 'Actinidia09111' => 'ach', 'Actinidia21141' => 'ach', 'Actinidia23463' => 'ach', 'Actinidia24921' => 'ach', 'Actinidia24922' => 'ach', 'Actinidia40217' => 'ach', 'Ah.02g111290' => 'amhyb', 'Ah.04g152990' => 'amhyb', 'Ah.04g154200' => 'amhyb', 'Ah.11g050260' => 'amhyb', 'AL1G12530' => 'aly', 'AL5G46170' => 'aly', 'AL6G50340' => 'aly', 'AL7G40080' => 'aly', 'AL7G41210' => 'aly', 'AL7G41220' => 'aly', 'Aqoxy1G04210' => 'aox', 'Aqoxy2G03208' => 'aox', 'Aqoxy2G03455' => 'aox', 'Aqoxy5G00411' => 'aox', 'Aqoxy5G00412' => 'aox', 'arahy.Tifrunner.gnm1.ann1.49SUU1' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MVS4C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.75IU33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.7I5NSS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ATYH9W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.EC8K22' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GYHR0X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3ASU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYC4V3' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QQX1F4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YV67XB' => 'arhy', 'AT1G03070' => 'ath', 'AT3G63310' => 'ath', 'AT4G02690' => 'ath', 'AT4G14730' => 'ath', 'AT4G15470' => 'ath', 'ATR0626G094' => 'atr', 'ATR0665G225' => 'atr', 'Atru.chr4.2679' => 'acertr', 'Atru.chr4.2686' => 'acertr', 'Atru.chr5.1505' => 'acertr', 'AUR62011978' => 'cqu', 'AUR62015307' => 'cqu', 'AUR62024088' => 'cqu', 'AUR62032290' => 'cqu', 'AUR62032746' => 'cqu', 'AUR62034690' => 'cqu', 'BcaB01g00405' => 'bca', 'BcaB01g01225' => 'bca', 'BcaB02g08066' => 'bca', 'BcaB03g15743' => 'bca', 'BcaB04g18297' => 'bca', 'BcaB05g23658' => 'bca', 'BcaC03g16164' => 'bca', 'BcaC03g16165' => 'bca', 'BcaC05g24640' => 'bca', 'BcaC05g28973' => 'bca', 'BcaC06g32935' => 'bca', 'BcaC06g33409' => 'bca', 'BcaC07g37887' => 'bca', 'BcaC08g43544' => 'bca', 'BcaC09g50149' => 'bca', 'BcaNung00341' => 'bca', 'BolC1t02775H' => 'bol', 'BolC2t09925H' => 'bol', 'BolC4t24523H' => 'bol', 'BolC5t28948H' => 'bol', 'BolC5t33853H' => 'bol', 'BolC6t38977H' => 'bol', 'BolC7t45237H' => 'bol', 'BolC9t57450H' => 'bol', 'BraA01t02202Z' => 'bra', 'BraA01t03179Z' => 'bra', 'BraA02t07482Z' => 'bra', 'BraA03t14007Z' => 'bra', 'BraA04t15731Z' => 'bra', 'BraA08t33168Z' => 'bra', 'BraA10t42446Z' => 'bra', 'C01p28510' => 'bna', 'C02p39160' => 'bna', 'C04p29920' => 'bna', 'C05p01690' => 'bna', 'C05p51670' => 'bna', 'C06p38840' => 'bna', 'C07p47160' => 'bna', 'C08p06130' => 'bna', 'CAN.G1410.2' => 'can', 'CAN.G1572.2' => 'can', 'CAN.G380.11' => 'can', 'CAN.G771.5' => 'can', 'CAN.G889.21' => 'can', 'CANSAT25G2266' => 'cansat', 'CANSAT78G1483' => 'cansat', 'CARHR002420' => 'chi', 'CARHR221210' => 'chi', 'CARHR222220' => 'chi', 'CARHR250990' => 'chi', 'CARHR291650' => 'chi', 'Carub.0001s0221' => 'cru', 'Carub.0005s2997' => 'cru', 'Carub.0006s3443' => 'cru', 'Carub.0007s2644' => 'cru', 'Carub.0007s2743' => 'cru', 'Ca_00597_v3' => 'car', 'Ca_08633_v3' => 'car', 'Ca_09733_v3' => 'car', 'Ca_11156_v3' => 'car', 'Ca_29018_v3' => 'car', 'CBR_g21764' => 'cbr', 'CBR_g39736' => 'cbr', 'Cc01_g19090' => 'ccan', 'Cc03_g02840' => 'ccan', 'Cc03_g04220' => 'ccan', 'CDE04G0862' => 'cde', 'CDE07G1902' => 'cde', 'CDE10G0481' => 'cde', 'Cfa006186' => 'cfa', 'Cfa015549' => 'cfa', 'Ciclev10005717m.g' => 'ccl', 'Ciclev10006442m.g' => 'ccl', 'Ciclev10021936m.g' => 'ccl', 'Ciclev10033906m.g' => 'ccl', 'CiPaw.01G157500' => 'cil', 'CiPaw.02G090000' => 'cil', 'CiPaw.02G121600' => 'cil', 'CiPaw.07G087900' => 'cil', 'CiPaw.08G108700' => 'cil', 'ClCG06G005680' => 'cla', 'ClCG06G006450' => 'cla', 'ClCG07G000450' => 'cla', 'ClCG09G007370' => 'cla', 'COL.COLO4_09045' => 'col', 'COL.COLO4_09046' => 'col', 'COL.COLO4_09200' => 'col', 'COL.COLO4_09849' => 'col', 'COL.COLO4_09851' => 'col', 'COL.COLO4_23805' => 'col', 'Cpa.g.sc16.58' => 'cpa', 'Cpa.g.sc44.116' => 'cpa', 'Cpa.g.sc52.112' => 'cpa', 'Cre01.g035450' => 'cre', 'Cre06.g252401' => 'cre', 'CsaV3_2G013450' => 'csa', 'CsaV3_2G013630' => 'csa', 'CsaV3_6G005470' => 'csa', 'CSS0009280' => 'camsi', 'CSS0009767' => 'camsi', 'CSS0015134' => 'camsi', 'CSS0023227' => 'camsi', 'CSS0032510' => 'camsi', 'CSS0038770' => 'camsi', 'CSS0042894' => 'camsi', 'CSS0048954' => 'camsi', 'CSS0050338' => 'camsi', 'DCAR_002426' => 'dca', 'DCAR_002707' => 'dca', 'DCAR_012503' => 'dca', 'DCAR_027241' => 'dca', 'Dinv14040' => 'din', 'Dinv22509' => 'din', 'Dinv32893' => 'din', 'Dinv38358' => 'din', 'Dinv44464' => 'din', 'Duzib133G0637' => 'dzi', 'Duzib138G1669' => 'dzi', 'Duzib151G0626' => 'dzi', 'Duzib212G0951' => 'dzi', 'ECA236G2642' => 'eca', 'ECA236G4094' => 'eca', 'ECA247G3967' => 'eca', 'ECA248G3971' => 'eca', 'EL10Ac3g06450' => 'bvu', 'EL10Ac3g06855' => 'bvu', 'EL10Ac5g10501' => 'bvu', 'EL10Ac5g10505' => 'bvu', 'Eucgr.H01413' => 'egr', 'Eucgr.H01638' => 'egr', 'Eucgr.H03417' => 'egr', 'Eucgr.H03636' => 'egr', 'Eucgr.K03330' => 'egr', 'FAN07G0592' => 'fan', 'FAN12G3048' => 'fan', 'FAN12G3470' => 'fan', 'FAN15G0878' => 'fan', 'FAN15G3017' => 'fan', 'FAN15G3274' => 'fan', 'FAN17G1349' => 'fan', 'FAN17G1853' => 'fan', 'FAN19G0938' => 'fan', 'FAN20G0507' => 'fan', 'FAN20G0749' => 'fan', 'FAN20G1155' => 'fan', 'FAN22G0667' => 'fan', 'FAN22G0781' => 'fan', 'FAN24G0059' => 'fan', 'FAN24G0651' => 'fan', 'FAN24G3542' => 'fan', 'FAN27G1868' => 'fan', 'FAN27G2236' => 'fan', 'FAN27G2537' => 'fan', 'FvH4_1g22950' => 'fve', 'FvH4_2g23060' => 'fve', 'FvH4_2g23070' => 'fve', 'FvH4_2g24870' => 'fve', 'FvH4_4g01040' => 'fve', 'FvH4_4g04411' => 'fve', 'FvH4_4g14100' => 'fve', 'FvH4_4g33780' => 'fve', 'FvH4_6g44540' => 'fve', 'Glyma.02G144700' => 'gma', 'Glyma.03G157100' => 'gma', 'Glyma.10G029400' => 'gma', 'Glyma.10G272600' => 'gma', 'Glyma.13G211300' => 'gma', 'Glyma.15G101400' => 'gma', 'Glyma.19G159300' => 'gma', 'Glyma.20G117300' => 'gma', 'Gohir.A02G044400' => 'ghi', 'Gohir.A08G045190' => 'ghi', 'Gohir.A08G064500' => 'ghi', 'Gohir.A08G187100' => 'ghi', 'Gohir.A09G060400' => 'ghi', 'Gohir.A10G106200' => 'ghi', 'Gohir.D02G050300' => 'ghi', 'Gohir.D08G055400' => 'ghi', 'Gohir.D08G073000' => 'ghi', 'Gohir.D08G205400' => 'ghi', 'Gohir.D09G059500' => 'ghi', 'Gohir.D10G162000' => 'ghi', 'Gorai.004G056000' => 'gra', 'Gorai.004G077400' => 'gra', 'Gorai.004G217400' => 'gra', 'Gorai.005G055600' => 'gra', 'Gorai.006G074200' => 'gra', 'Gorai.011G181100' => 'gra', 'GSVIVG01001203001' => 'vvi', 'GSVIVG01017864001' => 'vvi', 'GSVIVG01018035001' => 'vvi', 'HanXRQChr03g0079931' => 'han', 'HanXRQChr04g0113951' => 'han', 'HanXRQChr04g0113961' => 'han', 'HanXRQChr10g0281761' => 'han', 'HanXRQChr10g0281791' => 'han', 'HanXRQChr10g0281921' => 'han', 'HanXRQChr10g0281931' => 'han', 'HanXRQChr11g0337351' => 'han', 'HanXRQChr15g0480821' => 'han', 'Haze_01000' => 'cav', 'Haze_04657' => 'cav', 'Hma1.2p1_0511F.1_g169180' => 'hma', 'Hma1.2p1_0549F.1_g176940' => 'hma', 'Hma1.2p1_0643F.1_g194400' => 'hma', 'Hma1.2p1_0760F.1_g214000' => 'hma', 'Hma1.2p1_1924F.1_g307710' => 'hma', 'Hma1.2p1_2025F.1_g311470' => 'hma', 'HPP92_009616' => 'vpl', 'HPP92_015628' => 'vpl', 'HPP92_020351' => 'vpl', 'HPP92_024847' => 'vpl', 'HPP92_025235' => 'vpl', 'Hund02860' => 'sun', 'Hund20661' => 'sun', 'Hund22804' => 'sun', 'Lalb_Chr02g0142531' => 'lal', 'Lalb_Chr02g0145871' => 'lal', 'Lalb_Chr06g0162801' => 'lal', 'Lalb_Chr21g0308821' => 'lal', 'Lj1A51T16' => 'lonja', 'Lj1g0015199' => 'lja', 'Lj2A1166G39' => 'lonja', 'Lj2A1166T39' => 'lonja', 'Lj3A728T50' => 'lonja', 'Lj3A728T51' => 'lonja', 'Lj3C728G5' => 'lonja', 'Lj5g0016190' => 'lja', 'Lj5g0020674' => 'lja', 'Lj6A664T62' => 'lonja', 'Lj6g0017676' => 'lja', 'Lsat_1_v5_gn_5_184680' => 'lsa', 'Lsat_1_v5_gn_5_49321' => 'lsa', 'Lsat_1_v5_gn_7_25740' => 'lsa', 'Lsat_1_v5_gn_8_57181' => 'lsa', 'Lsat_1_v5_gn_9_7421' => 'lsa', 'Manes.01G204600' => 'mes', 'Manes.03G187000' => 'mes', 'Manes.03G187200' => 'mes', 'Manes.05G080700' => 'mes', 'Manes.05G080800' => 'mes', 'Manes.15G020800' => 'mes', 'Mapoly0093s0068' => 'mpo', 'MBI05_g00611_MAGBIO' => 'mbi', 'MBI11_g35359_MAGBIO' => 'mbi', 'MBI11_g47454_MAGBIO' => 'mbi', 'MBI11_g47455_MAGBIO' => 'mbi', 'MBI17_g17894_MAGBIO' => 'mbi', 'MBI18_g03005_MAGBIO' => 'mbi', 'MBI18_g03006_MAGBIO' => 'mbi', 'MBI19_g39900_MAGBIO' => 'mbi', 'MD03G1259200' => 'mdo', 'MD11G1279800' => 'mdo', 'MD13G1179700' => 'mdo', 'MD13G1198700' => 'mdo', 'MD16G1180700' => 'mdo', 'Medtr1g071430' => 'mtr', 'Medtr1g110390' => 'mtr', 'Medtr2g021130' => 'mtr', 'Medtr7g095510' => 'mtr', 'Medtr7g095530' => 'mtr', 'Medtr7g095550' => 'mtr', 'Medtr7g095600' => 'mtr', 'Medtr7g095620' => 'mtr', 'Medtr7g095640' => 'mtr', 'Medtr8g056770' => 'mtr', 'MELO3C014302.2' => 'cme', 'MELO3C015800.2' => 'cme', 'MELO3C021390.2' => 'cme', 'MELO3C031180.2' => 'cme', 'MELO3C031182.2' => 'cme', 'Migut.D00365' => 'egut', 'Migut.D00366' => 'egut', 'Migut.G00249' => 'egut', 'Migut.J01538' => 'egut', 'Migut.N00209' => 'egut', 'Migut.N02029' => 'egut', 'MSTRG.10023' => 'ama', 'MSTRG.12553' => 'ama', 'MSTRG.18260' => 'ama', 'MSTRG.18262' => 'ama', 'MSTRG.18263' => 'ama', 'MSTRG.21531' => 'ama', 'MSTRG.21873' => 'ama', 'Nitab4.5_0000057g0260' => 'nta', 'Nitab4.5_0000059g0070' => 'nta', 'Nitab4.5_0000090g0340' => 'nta', 'Nitab4.5_0000252g0270' => 'nta', 'Nitab4.5_0000535g0170' => 'nta', 'Nitab4.5_0000759g0270' => 'nta', 'Nitab4.5_0000871g0060' => 'nta', 'Nitab4.5_0001713g0040' => 'nta', 'Nitab4.5_0004355g0050' => 'nta', 'Nitab4.5_0006229g0010' => 'nta', 'Nn1g02432' => 'nnu', 'Nn4g26141' => 'nnu', 'Nn6g34155' => 'nnu', 'Oeu017775.1' => 'oeu', 'Oeu020885.1' => 'oeu', 'Oeu021630.1' => 'oeu', 'Oeu023627.1' => 'oeu', 'Oeu023650.1' => 'oeu', 'Oeu037662.1' => 'oeu', 'Oeu037678.1' => 'oeu', 'Os03g0745600' => 'osa', 'Os03g0795600' => 'osa', 'Os03g0795800' => 'osa', 'Os05g0402300' => 'osa', 'Os07g0177200' => 'osa', 'Os07g0177300' => 'osa', 'Os11g0581900' => 'osa', 'Peaxi162Scf00095g00715' => 'pax', 'Peaxi162Scf00152g01412' => 'pax', 'Peaxi162Scf00152g01434' => 'pax', 'Peaxi162Scf00152g01528' => 'pax', 'Peaxi162Scf00230g00067' => 'pax', 'Peaxi162Scf00316g00087' => 'pax', 'Peaxi162Scf00373g00116' => 'pax', 'Peaxi162Scf00783g00010' => 'pax', 'Peaxi162Scf28759g00003' => 'pax', 'PGR004G0698' => 'pgr', 'PGR044G0634' => 'pgr', 'PGR044G0859' => 'pgr', 'PGR044G1578' => 'pgr', 'PGR065G0003' => 'pgr', 'PGR119G0813' => 'pgr', 'PGSC0003DMG400006443' => 'stu', 'PGSC0003DMG400012777' => 'stu', 'PGSC0003DMG400013548' => 'stu', 'PGSC0003DMG400019313' => 'stu', 'PGSC0003DMG400020137' => 'stu', 'Phvul.001G154500' => 'pvu', 'Phvul.006G157400' => 'pvu', 'Phvul.007G029100' => 'pvu', 'Phvul.007G174500' => 'pvu', 'Potri.002G049000' => 'ptr', 'Potri.005G213900' => 'ptr', 'Potri.005G214000' => 'ptr', 'Potri.008G157100' => 'ptr', 'Potri.008G199200' => 'ptr', 'Potri.010G028900' => 'ptr', 'Pp3c15_13530' => 'ppa', 'Pp3c3_15530' => 'ppa', 'Pp3c4_29330' => 'ppa', 'Pp3c9_13460' => 'ppa', 'Prupe.1G020400' => 'ppe', 'Prupe.1G148200' => 'ppe', 'Prupe.8G235700' => 'ppe', 'Psat1g185200' => 'psa', 'Psat3g062240' => 'psa', 'Psat6g059200' => 'psa', 'Psat6g225960' => 'psa', 'PSO063G3473' => 'pso', 'PSO170G4363' => 'pso', 'PSO170G5982' => 'pso', 'PSO210G2362' => 'pso', 'PSO407G0333' => 'pso', 'PSO832G3557' => 'pso', 'QL06p001182' => 'qlo', 'QL06p005995' => 'qlo', 'QL12p020385' => 'qlo', 'RcHm_v2.0_Chr3g0491411' => 'rch', 'RcHm_v2.0_Chr4g0387621' => 'rch', 'RcHm_v2.0_Chr4g0419241' => 'rch', 'RcHm_v2.0_Chr5g0056651' => 'rch', 'RcHm_v2.0_Chr6g0290161' => 'rch', 'RcHm_v2.0_Chr6g0290181' => 'rch', 'RcHm_v2.0_Chr6g0290191' => 'rch', 'RcHm_v2.0_Chr6g0292711' => 'rch', 'Rhsim01G0272300' => 'rsi', 'Rhsim04G0212000' => 'rsi', 'Rhsim04G0239700' => 'rsi', 'Rhsim13G0028100' => 'rsi', 'Sabra02G0039900' => 'sbr', 'Sabra05G0163500' => 'sbr', 'Sabra05G0163600' => 'sbr', 'Sabra08G0119600' => 'sbr', 'Sabra08G0161400' => 'sbr', 'Sabra10G0012100' => 'sbr', 'SalBow2G1365' => 'sbo', 'SalBow3G2474' => 'sbo', 'SalBow4G0947' => 'sbo', 'SalBow6G0359' => 'sbo', 'SalBow6G2107' => 'sbo', 'Sc13g0003820' => 'sci', 'Sc14g0006470' => 'sci', 'Sc17g0001210' => 'sci', 'Sc19g0003990' => 'sci', 'Sc19g0004000' => 'sci', 'Sc24g0004250' => 'sci', 'Sc25g0004260' => 'sci', 'Sed0001185' => 'sed', 'Sed0007882' => 'sed', 'Sed0021272' => 'sed', 'Sed0025302' => 'sed', 'SEGI_05464' => 'sgi', 'SEGI_05980' => 'sgi', 'SEGI_17626' => 'sgi', 'SEGI_27197' => 'sgi', 'SEGI_31601' => 'sgi', 'SGA_v2.0_scaffold138G35302' => 'sas', 'SGA_v2.0_scaffold1G00526' => 'sas', 'SGA_v2.0_scaffold237G43844' => 'sas', 'SGA_v2.0_scaffold308G48123' => 'sas', 'SGA_v2.0_scaffold80G25924' => 'sas', 'SMO141G0309' => 'smo', 'SMO340G0169' => 'smo', 'SMO351G0394' => 'smo', 'Solyc01g080330.4' => 'sly', 'Solyc06g084130.3' => 'sly', 'Solyc07g042510.3' => 'sly', 'Solyc09g065610.2' => 'sly', 'Solyc09g082590.4' => 'sly', 'Sopen01g032130' => 'spe', 'Sopen06g035510' => 'spe', 'Sopen09g027360' => 'spe', 'Sopen09g031450' => 'spe', 'Sp1g02070' => 'spa', 'Sp5g00220' => 'spa', 'Sp6g02610' => 'spa', 'Sp7g12840' => 'spa', 'Sp7g13690' => 'spa', 'TAR362G0052' => 'tar', 'TAR362G1184' => 'tar', 'TAR365G0805' => 'tar', 'TAR365G1149' => 'tar', 'TAR633G0831' => 'tar', 'TAR636G1986' => 'tar', 'THA.LOC104802548' => 'tha', 'THA.LOC104817565' => 'tha', 'THA.LOC104820223' => 'tha', 'THA.LOC104821757' => 'tha', 'THA.LOC104825988' => 'tha', 'Thecc.01G272700' => 'tca', 'Thecc.04G271000' => 'tca', 'Thecc.07G010600' => 'tca', 'Thecc.07G010700' => 'tca', 'Thecc.07G010800' => 'tca', 'Thecc.07G010900' => 'tca', 'Thhalv10006212m.g' => 'esa', 'Thhalv10008600m.g' => 'esa', 'Thhalv10026042m.g' => 'esa', 'Thhalv10026089m.g' => 'esa', 'Thhalv10028915m.g' => 'esa', 'TPR.G10225' => 'tpr', 'TPR.G18024' => 'tpr', 'TPR.G19114' => 'tpr', 'TPR.G25704' => 'tpr', 'TPR.G32519' => 'tpr', 'TPR.G4914' => 'tpr', 'TWI09G1227' => 'twi', 'TWI53G0774' => 'twi', 'TWI73G0539' => 'twi', 'TWI75G1113' => 'twi', 'unitig_22.g5272' => 'ugi', 'unitig_736.g22498' => 'ugi', 'vmacro02604' => 'vma', 'vmacro08248' => 'vma', 'vmacro14856' => 'vma', 'vmacro14891' => 'vma', 'vmacro14897' => 'vma', 'vmacro14898' => 'vma', 'vmacro14899' => 'vma', 'vmacro14900' => 'vma', 'vmacro17997' => 'vma', 'VMungo0540G2357' => 'vmu', 'VMungo0720G0346' => 'vmu', 'VMungo0720G2030' => 'vmu', 'VMungo1383G2250' => 'vmu', 'Zm00001eb057010' => 'zma', 'Zm00001eb060650' => 'zma', 'Zm00001eb060660' => 'zma', 'Zm00001eb200530' => 'zma', 'Zm00001eb212980' => 'zma', 'Zm00001eb212990' => 'zma', 'Zm00001eb215030' => 'zma', 'Zm00001eb287610' => 'zma', 'Zm00001eb301240' => 'zma' ) $gf_id = 'HOM05D001150' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001150' ) $data_identifier = 'HOM05D001150' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 6, 'amhyb' => (int) 4, 'aly' => (int) 6, 'aox' => (int) 5, 'arhy' => (int) 11, 'ath' => (int) 5, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 5, 'cansat' => (int) 2, 'chi' => (int) 5, 'cru' => (int) 5, 'car' => (int) 5, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 4, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 9, 'dca' => (int) 4, 'din' => (int) 5, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 4, 'egr' => (int) 5, 'fan' => (int) 20, 'fve' => (int) 9, 'gma' => (int) 8, 'ghi' => (int) 12, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 9, 'cav' => (int) 2, 'hma' => (int) 6, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 4, 'lonja' => (int) 7, 'lja' => (int) 4, 'lsa' => (int) 5, 'mes' => (int) 6, 'mpo' => (int) 1, 'mbi' => (int) 8, 'mdo' => (int) 5, 'mtr' => (int) 10, 'cme' => (int) 5, 'egut' => (int) 6, 'ama' => (int) 7, 'nta' => (int) 10, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 7, 'pax' => (int) 9, 'pgr' => (int) 6, 'stu' => (int) 5, 'pvu' => (int) 4, 'ptr' => (int) 6, 'ppa' => (int) 4, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 6, 'qlo' => (int) 3, 'rch' => (int) 8, 'rsi' => (int) 4, 'sbr' => (int) 6, 'sbo' => (int) 5, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 5, 'sas' => (int) 5, 'smo' => (int) 3, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 5, 'tca' => (int) 6, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 9, 'vmu' => (int) 4, 'zma' => (int) 9 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb301240' $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